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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")
In most cases, you don't need to download the package archive at all.
ensembldb
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ensembldb.
Utilities to create and use an Ensembl based annotation database
Bioconductor version: 3.3
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.
Author: Johannes Rainer <johannes.rainer at eurac.edu>, Tim Triche <tim.triche at usc.edu>
Maintainer: Johannes Rainer <johannes.rainer at eurac.edu>
Citation (from within R,
enter citation("ensembldb")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")
Documentation
| HTML | R Script | Generating an using Ensembl based annotation packages |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | AnnotationData, Coverage, Genetics, Sequencing, Software |
| Version | 1.4.7 |
| In Bioconductor since | BioC 3.1 (R-3.2) (1.5 years) |
| License | LGPL |
| Depends | BiocGenerics(>= 0.15.10), GenomicRanges(>= 1.23.21), GenomicFeatures(>= 1.23.18) |
| Imports | methods, RSQLite, DBI, Biobase, GenomeInfoDb, AnnotationDbi(>= 1.31.19), rtracklayer, S4Vectors, AnnotationHub, Rsamtools, IRanges |
| LinkingTo | |
| Suggests | BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75(>= 0.99.7), RUnit, shiny, Gviz, BSgenome.Hsapiens.UCSC.hg19 |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/jotsetung/ensembldb |
| BugReports | https://github.com/jotsetung/ensembldb/issues |
| Depends On Me | EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v75, EnsDb.Mmusculus.v79, EnsDb.Rnorvegicus.v75, EnsDb.Rnorvegicus.v79 |
| Imports Me | biovizBase, ChIPpeakAnno, ggbio |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ensembldb_1.4.7.tar.gz |
| Windows Binary | ensembldb_1.4.7.zip |
| Mac OS X 10.9 (Mavericks) | ensembldb_1.4.7.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ensembldb/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/ensembldb/ |
| Package Downloads Report | Download Stats |
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